Distinguishing regional from within-codon rate heterogeneity in DNA sequence alignments

Mantzaris, A.V. and Husmeier, D. (2009) Distinguishing regional from within-codon rate heterogeneity in DNA sequence alignments. Lecture Notes in Computer Science, 5780, pp. 187-198. (doi: 10.1007/978-3-642-04031-3_17)

Abstract

We present an improved phylogenetic factorial hidden Markov model (FHMM) for detecting two types of mosaic structures in DNA sequence alignments, related to (1) recombination and (2) rate heterogeneity. The focus of the present work is on improving the modelling of the latter aspect. Earlier papers have modelled different degrees of rate heterogeneity with separate hidden states of the FHMM. This approach fails to appreciate the intrinsic difference between two types of rate heterogeneity: long-range regional effects, which are potentially related to differences in the selective pressure, and the short-term periodic patterns within the codons, which merely capture the signature of the genetic code. We propose an improved model that explicitly distinguishes between these two effects, and we assess its performance on a set of simulated DNA sequence alignments.

• Item Type: Articles
• Additional Information: The original publication is available at www.springerlink.com<p/> Issue title: Pattern Recognition in Bioinformatics
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Husmeier, Professor Dirk
• Authors: Mantzaris, A.V., and Husmeier, D.
• College/School: College of Science and Engineering > School of Mathematics and Statistics > Statistics
• Journal Name: Lecture Notes in Computer Science
• Publisher: Springer
• ISSN: 0302-9743
• Copyright Holders: Copyright © 2009 Springer
• First Published: First published in Lecture Notes in Computer Science 5780
• Publisher Policy: Reproduced in accordance with the copyright policy of the publisher